how to pick a h-bond ?
Serge Smirnov L.
serge at amadeus
Fri Dec 1 13:51:05 EST 1995
Do you have any idea how I can pick a hydrogen bond and call its energy and
geometry parameters within an XPLOR-program?
Let's suppose that I'm given by two atoms (their id's are $1 and $2). F.e. one
of them is N, and the other is O (ChemType). I don't know which is a donor and
which is an acceptor. Of course, in my topology file I described all donors and
all acceptor. (I just have no idea how to get this information back within
XPLOR's programs.) I don't even know if there is a h-bond between these two
The way I'm using now is:
structure @my.psf end
coor @my.pdb end
! Only H-bond energy is calculated
exclude * include hbon
! acceptor - antecedent distance; in Angstroms
eval ($AAA = 1.6)
!Only atoms within $AAA sphere around $1 and $2 are taken into consideration
!I suppose here that the longest covalent bond is shorte than $AAA
!At the same time I suppose that there are only relevant atoms within
! such a sphere. But this may be not true sometimes.
(id $1 around $AAA)
(id $2 around $AAA)
! forget previous energy terms
energy accumulate=reset end
! get H_bond energy
energy accumulate=energy end
! if h-bond energy not zero pick $1 and $2 and .... ? how to get the hydrogen?
if ($HBON<0) then
(id $1) (id $2) geometry
This way is rather ambiguous one. Within the spheres perhaps there are other
O's, N's, H's, etc. So, I can be confused by the value of H-bond energy.
Unfortunately PRINT HBON statement is not a solution here, 'cause it doesn't
allow to use the information about the h-bond _within_ the program itself. It
only gives me an opportunity to store the information in some other file and
then, after the program stops, use it.
I would greatly appreciate if somebody gives me a hint how to determine the
hydrogen and the acceptor antecedent in the case described above...
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